Overview-of-RCy3.R
In RCy3: Functions to Access and Control Cytoscape

## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
  eval=FALSE
)

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#  if(!"RCy3" %in% installed.packages()){
#      install.packages("BiocManager")
#      BiocManager::install("RCy3")
#  }
#  library(RCy3)

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#      cytoscapePing ()
#      cytoscapeVersionInfo ()

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#  nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
#             group=c("A","A","B","B"), # categorical strings
#             score=as.integer(c(20,10,15,5)), # integers
#             stringsAsFactors=FALSE)
#  edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
#             target=c("node 1","node 2","node 3","node 3"),
#             interaction=c("inhibits","interacts","activates","interacts"),  # optional
#             weight=c(5.1,3.0,5.2,9.9), # numeric
#             stringsAsFactors=FALSE)
#  
#  createNetworkFromDataFrames(nodes,edges, title="my first network", collection="DataFrame Example")

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#  setVisualStyle('Marquee')

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#  style.name = "myStyle"
#  defaults <- list(NODE_SHAPE="diamond",
#                   NODE_SIZE=30,
#                   EDGE_TRANSPARENCY=120,
#                   NODE_LABEL_POSITION="W,E,c,0.00,0.00")
#  nodeLabels <- mapVisualProperty('node label','id','p')
#  nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA"))
#  arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',c("activates","inhibits","interacts"),c("Arrow","T","None"))
#  edgeWidth <- mapVisualProperty('edge width','weight','p')
#  
#  createVisualStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth))
#  setVisualStyle(style.name)

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#      g = new ('graphNEL', edgemode='directed')
#      g = graph::addNode ('A', g)
#      g = graph::addNode ('D', g)
#      g = graph::addNode ('C', g, edges = list('D'))
#      g = graph::addNode ('B', g, edges = list(c('A','D','C')))
#      createNetworkFromGraph (g, title='simple network', collection='GraphNEL Example')

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#      df <- data.frame (moleculeType=c('kinase','TF','cytokine','cytokine'),
#                       log2fc=c(1.8,3.0,-1.2,-2.5),
#                       row.names = c('A','B','C','D'), # row.names = node names
#                       stringsAsFactors = FALSE)       # important when loading strings!
#      loadTableData (df)

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#      setNodeShapeDefault ('OCTAGON')
#      setNodeColorDefault ('#AAFF88')
#      setNodeSizeDefault  (60)
#      setNodeFontSizeDefault (30)

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#      getNodeShapes ()   # diamond, ellipse, trapezoid, triangle, etc.
#      column <- 'moleculeType'
#      values <- c ('kinase',  'TF','cytokine')
#      shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE')
#      setNodeShapeMapping (column, values, shapes)

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#      column <- 'log2fc'
#      control.points <- c (-3.0, 0.0, 3.0)
#      colors <-  c ('#5588DD', '#FFFFFF', '#DD8855')
#      setNodeColorMapping (column, control.points, colors)

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#      control.points <- c (-2.0, 0.0, 2.0)
#      colors <-  c ('#2255CC', '#5588DD', '#FFFFFF', '#DD8855','#CC5522')
#      setNodeColorMapping (column, control.points, colors)

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#      control.points = c (-3.0, 2.0, 3.0)
#      sizes     = c (20, 80, 90)
#      setNodeSizeMapping (column, control.points, sizes)
#  

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#      selectNodes ('C','name')

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#      getSelectedNodes ()

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#      selectFirstNeighbors ()

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#      node.names <- getSelectedNodes ()

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#      clearSelection()
#      ?clearSelection

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#      saveSession('vignette_session') #.cys

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#      full.path=paste(getwd(),'vignette_image',sep='/')
#      exportImage(full.path, 'PNG', zoom=200) #.png scaled by 200%
#      exportImage(full.path, 'PDF') #.pdf
#      ?exportImage

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#  help(package=RCy3)

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#  cyrestAPI()  # CyREST API
#  commandsAPI()  # Commands API

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#  commandsHelp("help")

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#  commandsHelp("help network")

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#  commandsHelp("help network select")

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#  browseVignettes("RCy3")